BioC 3.5: CHECK report for rDGIdb on tokay2

Package: rDGIdb

Version: 1.2.1

Command: rm -rf rDGIdb.buildbin-libdir rDGIdb.Rcheck && mkdir rDGIdb.buildbin-libdir rDGIdb.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rDGIdb.buildbin-libdir rDGIdb_1.2.1.tar.gz >rDGIdb.Rcheck\00install.out 2>&1 && cp rDGIdb.Rcheck\00install.out rDGIdb-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=rDGIdb.buildbin-libdir --install="check:rDGIdb-install.out" --force-multiarch --no-vignettes --timings rDGIdb_1.2.1.tar.gz

StartedAt: 2017-09-19 02:13:13 -0400 (Tue, 19 Sep 2017)

EndedAt: 2017-09-19 02:14:02 -0400 (Tue, 19 Sep 2017)

EllapsedTime: 48.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: rDGIdb.Rcheck

Warnings: NA

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###
### Running command:
###
###   rm -rf rDGIdb.buildbin-libdir rDGIdb.Rcheck && mkdir rDGIdb.buildbin-libdir rDGIdb.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rDGIdb.buildbin-libdir rDGIdb_1.2.1.tar.gz >rDGIdb.Rcheck\00install.out 2>&1 && cp rDGIdb.Rcheck\00install.out rDGIdb-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=rDGIdb.buildbin-libdir --install="check:rDGIdb-install.out" --force-multiarch --no-vignettes --timings rDGIdb_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/rDGIdb.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rDGIdb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rDGIdb' version '1.2.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'rDGIdb' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'rDGIdb-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotInteractionsBySource
> ### Title: Interactions by source
> ### Aliases: plotInteractionsBySource
> ### Keywords: ˜aplot ˜device
> 
> ### ** Examples
> 
> queryResult <- queryDGIdb('KRAS')
Querying DGIDB...Error in queryDgidbPost(genes, interactionSources = databases, geneCategories = categories,  : 
  Oops, badly formatted query.
Calls: queryDGIdb -> queryDgidbPost
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'rDGIdb-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotInteractionsBySource
> ### Title: Interactions by source
> ### Aliases: plotInteractionsBySource
> ### Keywords: ˜aplot ˜device
> 
> ### ** Examples
> 
> queryResult <- queryDGIdb('KRAS')
Querying DGIDB...Error in queryDgidbPost(genes, interactionSources = databases, geneCategories = categories,  : 
  Oops, badly formatted query.
Calls: queryDGIdb -> queryDgidbPost
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1 
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3: stop("Oops, badly formatted query.")
  
  2. Error: Returns the right result (@test.queryDGIdb.R#27) ---------------------
  Oops, badly formatted query.
  1: queryDgidbPost(genes = c("XYZA", "BRAF"), interactionSources = "ChEMBL,MyCancerGenome", 
         geneCategories = "clinically actionable", interactionTypes = "n/a,inhibitor") at testthat/test.queryDGIdb.R:27
  2: stop("Oops, badly formatted query.")
  
  testthat results ================================================================
  OK: 15 SKIPPED: 0 FAILED: 2
  1. Error: Query DGIdb and result summary works (@test.queryDGIdb.R#21) 
  2. Error: Returns the right result (@test.queryDGIdb.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1 
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3: stop("Oops, badly formatted query.")
  
  2. Error: Returns the right result (@test.queryDGIdb.R#27) ---------------------
  Oops, badly formatted query.
  1: queryDgidbPost(genes = c("XYZA", "BRAF"), interactionSources = "ChEMBL,MyCancerGenome", 
         geneCategories = "clinically actionable", interactionTypes = "n/a,inhibitor") at testthat/test.queryDGIdb.R:27
  2: stop("Oops, badly formatted query.")
  
  testthat results ================================================================
  OK: 15 SKIPPED: 0 FAILED: 2
  1. Error: Query DGIdb and result summary works (@test.queryDGIdb.R#21) 
  2. Error: Returns the right result (@test.queryDGIdb.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 ERRORs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/rDGIdb.Rcheck/00check.log'
for details.

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(rDGIdb)
> 
> test_check("rDGIdb")
Querying DGIDB...done!
Querying DGIDB...done!
Querying DGIDB...1. Error: Query DGIdb and result summary works (@test.queryDGIdb.R#21) ---------
Oops, badly formatted query.
1: queryDGIdb(genes = "BRAF") at testthat/test.queryDGIdb.R:21
2: queryDgidbPost(genes, interactionSources = databases, geneCategories = categories, 
       interactionTypes = interactions)
3: stop("Oops, badly formatted query.")

2. Error: Returns the right result (@test.queryDGIdb.R#27) ---------------------
Oops, badly formatted query.
1: queryDgidbPost(genes = c("XYZA", "BRAF"), interactionSources = "ChEMBL,MyCancerGenome", 
       geneCategories = "clinically actionable", interactionTypes = "n/a,inhibitor") at testthat/test.queryDGIdb.R:27
2: stop("Oops, badly formatted query.")

testthat results ================================================================
OK: 15 SKIPPED: 0 FAILED: 2
1. Error: Query DGIdb and result summary works (@test.queryDGIdb.R#21) 
2. Error: Returns the right result (@test.queryDGIdb.R#27) 

Error: testthat unit tests failed
Execution halted

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(rDGIdb)
> 
> test_check("rDGIdb")
Querying DGIDB...done!
Querying DGIDB...done!
Querying DGIDB...1. Error: Query DGIdb and result summary works (@test.queryDGIdb.R#21) ---------
Oops, badly formatted query.
1: queryDGIdb(genes = "BRAF") at testthat/test.queryDGIdb.R:21
2: queryDgidbPost(genes, interactionSources = databases, geneCategories = categories, 
       interactionTypes = interactions)
3: stop("Oops, badly formatted query.")

2. Error: Returns the right result (@test.queryDGIdb.R#27) ---------------------
Oops, badly formatted query.
1: queryDgidbPost(genes = c("XYZA", "BRAF"), interactionSources = "ChEMBL,MyCancerGenome", 
       geneCategories = "clinically actionable", interactionTypes = "n/a,inhibitor") at testthat/test.queryDGIdb.R:27
2: stop("Oops, badly formatted query.")

testthat results ================================================================
OK: 15 SKIPPED: 0 FAILED: 2
1. Error: Query DGIdb and result summary works (@test.queryDGIdb.R#21) 
2. Error: Returns the right result (@test.queryDGIdb.R#27) 

Error: testthat unit tests failed
Execution halted

install for i386

* installing *source* package 'rDGIdb' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'rDGIdb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rDGIdb' as rDGIdb_1.2.1.zip
* DONE (rDGIdb)

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